I'll compare them game by game.

FF1 - Knights are better than Ninjas.
FF3 - Ninjas are better than Knights.
FF4 - Cecil is far better than Edge.
FF5 - Knights are better than Ninjas (barely though).
FF6 - Shadow is better than Cyan.
FF7 - I guess Cloud counts as a Knight. In which case, he's better than Yuffie.
FF9 - This one's close, but I liked Steiner more than Amarant.

Final Score: Knights 5, Ninjas 2.

Both are great classes, but Knights are generally better, I find.